Steve vs the Intersect
by CarsAndTelephones
Summary: Stephen Bartowski never wanted Chuck to become a spy. He never wanted the Intersect anywhere near his son. So what happens when Chuck uploads 2.0? Missing scene between seasons 2 and 3.


_AN—This piece has been floating around my hard drive for quite a while, and I finally decided I'd post it just because :) I wrote it mainly because I wanted to give Stephen Bartowski a chance to lament Chuck's decision at the end of Season 2, because they seemed to have forgotten about him at the beginning of Season 3 (Though I hear we're getting more Steve soon!). Anyway, thanks for taking a peak at this and please review!_

_Disclaimer—I don't own Chuck, Sarah, Casey, or Orion, as much as I love them all._

**Steve vs. the Intersect**

Steve sat on the edge of the fountain in the middle of the tiny courtyard. He hadn't moved from that spot in hours and didn't plan on moving until he knew for certain that all was right—it didn't matter that his legs had gone numb from chill or that he was exhausted to the core. He sat with elbows propped on knees, back bent slightly forward, hands clasped in front of his face, forever gazing at the gate at the entrance. The ruins of the reception still littered the ground, brightly colored flowers and streamers lying haphazardly over the stones, and the lights strung across the enclosure still casting a friendly glow over the empty yard, a tantalizing reminder of what had been a beautiful celebration. The fountain trickled into the pool at the bottom with a quiet chuckling sound, and the rest of the enclosure remained peacefully silent, but none of this warmth reached the silent figure in the center of it at all. He was alone with his thoughts.

When the sound of a door opened behind him, he twisted quickly in his place, convinced for a second that the very person he was waiting for had somehow escaped his notice and had been waiting for him inside all this time. But when he turned, he saw that it was only Eleanor, still resplendent in her white wedding gown, mahogany hair piled elegantly on top of her head, and something deeper in her eyes—a look of extreme contentment that extended through her entire being. She stood in the doorway of the apartment, beaming out at him and clearly delirious with happiness. He couldn't help but smile slightly back despite his worry.

Ellie was beautiful.

"Dad!" she said, picking her way through fallen light baubles and half-wilted begonias, "What are you still doing up? Come inside—it's late." She settled herself gracefully on the ledge beside him, her bare feet poking slightly out from underneath the folds of her dress.

"I'm just waiting for your brother," he said with a smile, "I needed to talk to him about something. I'll be fine. You go on inside."

Ellie returned his smile with a warmth that seemed to brighten the courtyard tenfold. "Dad, Chuck's probably off somewhere with Sarah or—God forbid—_Morgan_. You can talk to him in the morning—he'll still be here. You should come inside."

"Nah, Eleanor," Steve said, chuckling without any real humor, "I just need to clear my head for a bit. Go on—Devon's probably waiting for you."

"Well," said Ellie, considering him, that absolute happiness still blazing out of her, "All right, but don't sit out here all night, okay?" She patted his arm gently.

"I'll do my best," he replied, catching her hand and looking up at her as she rose to her feet. "Goodnight." He paused before adding, "I love you, Eleanor."

She smiled wider. "I love you, too, Dad."

And with that, she bent and kissed him on the cheek, then turned and left to go back inside the apartment. He watched her retreating back a little wistfully.

He had missed his children growing up. He hadn't been there for their triumphs or their sorrows. He hadn't been there while Ellie had gone off to college and he hadn't been there for Chuck's graduation from high school. He hadn't been there for his daughter while she had struggled through med school and he hadn't been there to help his son when Stanford kicked him out. He hadn't been there for all those moments—those big decisions and life-altering choices when they needed a parent the most. He hadn't even been there for the small moments—the moments that really counted; the ones that he could look back upon and smile—like Ellie bringing home another perfect four-point from school or discussing the latest _Star Trek_ with Chuck. They had done that on their own. They had raised themselves and he hadn't had a hand in it. He had abandoned and disappointed them.

_You did it to save them,_ he told himself firmly, _If you hadn't left when you did, anyone—Fulcrum, the CIA, the NSA—could have used them, or worse, hurt them, all in an effort to get to you. You did what was best. You did what you had to do._

And yet a crippling sadness coiled around the pit of his stomach mixing with the worry that already permanently resided there. He had missed the things that mattered the most. He had to leave when he wanted above all else to stay—but doing anything else would have been selfish… and dangerous.

But now…

Charles, his son, had gotten involved in the very thing that he had sought to protect him from. Even with the Intersect out of his head, Chuck still threw himself into danger. He had gone after Bryce and Sarah without a thought.

_Why did he have to leave?_ Steve asked himself over and over again. But if he was honest with himself, he already knew the answer.

Because Chuck was a good person. Because he was acting selflessly—out of love. Because _everything_ that motivated Chuck came from love of family and friends.

And Steve felt a fierce pride of his son wash over him. Despite being free of the Intersect, Chuck had chosen not to stand by and watch his friends fall into danger. He had gone without question because that was simply who he was.

Now, all Steve could hope was that Chuck had survived the night. He had been gone for hours, and Steve knew all too well what could happen in that time—but he fought the queasiness in his stomach down when he thought of Chuck's team. Sarah and Casey would never let any harm come to that kid—of that he was certain. He knew beyond a doubt that Chuck had, however unintentionally, commanded a deep loyalty in both his handlers a long time ago simply by being himself. And Sarah—Steve was sure that the agent was in love with his son. Surely she wouldn't let anything happen to him. Surely they would all come out of this mess alive…

The sudden creak of the gate startled Steve from his thoughts, and he jumped up from the ledge of the fountain, pacing towards the entrance before he had fully realized who had come through.

"Charles," he called, as his son stepped out of the shadows of the archway. Chuck came forward wearily, and Steve clasped his son's stooped shoulders roughly, checking him over for any sign of injury.

"Dad," Chuck muttered, "I'm all right, it's okay…" He was clearly exhausted and his mussed suit hung off of him like he had been wearing it for years instead of days.

"What happened? Did you stop them?" said Steve, unable to keep the anxiousness out of his voice.

"Yeah…" Chuck's eyes were deadened. "Yeah, we stopped 'em…"

"Charles," Steve demanded, tightening his grip on his son's shoulders, "What happened?"

"Dad," he began, "Bryce is dead… We couldn't save him. We… we were too late."

Momentary shock washed over Steve and he searched his son's face for visual confirmation that what he had said was true. One look in Chuck's eyes was enough to know… and it made Steve feel sick. He should be used to this by now, he told himself, in his line of work. But somehow the death of someone that he had seen alive and well not hours before still came as a horrible jolt. Bryce Larkin… dead. Bryce Larkin the superspy, Bryce Larkin who had gained his trust a long time ago, Bryce Larkin who, despite being involved in something twisted, was a genuinely good man. He hadn't deserved the lot that he had gotten…

"I'm—I'm sorry, son," Steve said quietly.

Chuck swallowed. "He—he told me before he died that I should destroy the new Intersect. He said that it was too powerful… We were alone in the room… Sarah and Casey were outside—they were pinned down. Dad, I—I didn't know what to do…"

Steve furrowed his brow in confusion. His son seemed to be trying to tell him something—something that he felt guilty about… but he couldn't imagine what. "Charles, if you're saying that you destroyed the Intersect without anyone having uploaded it, I'm not angry. I would rather it was destroyed than given to the wrong people… I never meant it to be used as a weapon…"

"No—Dad, I—that's not what I meant," Chuck took a deep breath and looked straight into Steve's eyes.

An inkling of Chuck's true meaning brushed Steve's mind, but he quickly shook it away. "What are you saying, Charles?"

"Dad, I—" he faltered, hesitated and then plunged on, "Dad, I uploaded it."

The sentence hung between them heavily.

Steve's hands dropped from his son's shoulders.

"I'm sorry, Dad, I—" Chuck stuttered, struggling to explain himself, "How could I let that information go without it being used for good? Without using it how it was _supposed_ to be used? How could I turn my back on that and destroy it all knowing that it could—well—that it could save a lot of people?" His words came out in a desperate rush.

Steve didn't know what to say anymore. The world seemed to be pressing in around him. Here it was _again_—the very thing he had created coming back to haunt him in a way he had never anticipated. He had never wanted his son to come anywhere _near_ the Intersect—he had spent most of his adult life trying to protect those he loved from it and yet, like some horrible Tolkienian monster, it resurfaced again, and again, and again. Just when he had been beginning to relax, just when he thought his family was safe again, it reared its ugly head, waiting to swallow him in another current of life-altering circumstances and deadly consequences.

"Charles…" he began, not really knowing what he wanted to say, "You… I thought you wanted…"

"I did, Dad, but…" Chuck seemed to be struggling just as much as he was, "I can be so much _more_ than I am—with the Intersect, I can help people, I can be something bigger than… just Chuck Bartowski."

"But Charles, you _are _Chuck Bartowski—with or without the Intersect, son!" The fear was back again in the pit of Steve's stomach, but this time it would not be placated or vanished.

"Dad, I… I wanted this. I couldn't just—I couldn't just turn my back on all those people who might need my help—or need what's in my head."

"Son, the Intersect is _dangerous_—you know that better than anyone else! It touches _everyone_ remotely involved with it! Look at what happened to me! Look at our family, Chuck! Roark almost killed you, and he _wanted_ to kill Ellie as well—it was only good luck that saved us in the end! Charles… if I lost you or your sister, I—" Steve could not bring himself to finish the sentence. The consequence was too horrible to contemplate.

Chuck looked at him, the same determined spark deep in his eyes that had appeared earlier that same night when he had followed Sarah to Bryce. "That won't happen," he said. It was a statement of fact.

It was clear from his tone that Chuck would not be convinced otherwise—and anyway there was no point in arguing about it any further. What was done was done. Steve changed his tack abruptly. "They changed the schematics. It does something different now—even Bryce was wary of it. What does it do?"

To his deep surprise, Chuck actually smiled. It was a nervous half-smile, but it was a smile all the same. "Well," he began, suddenly shifting on his feet, "It—uh—it does something pretty awesome."

Steve raised his eyebrows, waiting.

"I took out five guys, Dad, _five!_" Chuck burst out, grinning like a little boy despite the seriousness of the situation and punching the air.

The eyebrows contracted. "_Physical_ flashes?"

"Yeah," Chuck replied, the grin still half-plastered on his face, and something almost like guilt intruding as well. "Yeah, pretty much."

Steve felt himself heaving an exhausted sigh, and he vaguely saw as Chuck rushed forward to help him towards the fountain once more. He lowered himself onto the ledge, and Chuck sat beside him, worry clouding the young man's features. But Steve didn't look at him as a whole new torrent of emotion drowned his already overwhelmed body.

Physical flashes… It was—impossible, improbable… absurd. It was meant to turn an experienced spy into a superhuman and a supercomputer at the same time. It was too much power for one person… but what did this mean for Chuck? Surely they would not let him go. Surely they meant to train him, to hound him until he either broke or turned into the superspy they wanted him to be. A horrifying image rose before him not of his Charles but of a cold, emotionless special agent, a heartless killer—one so far from his version of his son that they could not be considered remotely the same person.

"They want to train you," he said quietly to his hands. It was not a question.

"Yeah," Chuck replied, the worry still creasing his brow, "I'm supposed to leave for Prague tomorrow…"

"Charles, they will change you." He looked directly into his son's eyes when he said it. "They will turn you into something so far from yourself that you won't recognize who it is that walks out of that training facility. That's what they do. They'll turn you into a killer, son, and I… I can't stand by and let that happen."

Chuck stared at his father, the anxiety so apparent on his features. He had always been like that, Steve reflected. He could never hide his emotions, no matter how hard he tried. A glimmer of hope flickered behind Steve's concern. Perhaps Chuck's emotions would be his saving grace. "Dad," Chuck began, looking Steve in the eye, "I know what you've seen of the CIA, and I know what you think of spies—but I'm never gonna be a killer. I don't ever wanna be that—you gotta believe me."

Steve looked at his son, felt the sincerity in his tone, and saw it reflected in his face. "I do," he said after a moment, "I _do_ believe you, Charles."

They sat at the fountain for another prolonged moment, father and son together in silence. Then Steve shifted, his hands braced on his knees and turned to Chuck once more.

"Son," he said, absolute weariness hanging off his every word, "I can't come with you. You know that. But I can understand the decision that you made. Doesn't mean I'm happy about it, but—when the day comes that you need that thing out of your head again… I'll be there. You can count on that, Charles… In the meantime, promise me… promise me you'll look out for yourself."

Chuck fixed him with a far away stare.

"I promise, Dad."

Though the words were just that—words, Steve still felt somehow reassured. His son never said anything that wasn't truly from the heart. He would have faith in Chuck—because Chuck had never let him down. He heaved another sigh and rose from the fountain's edge. "Good," he said, "good."

Chuck rose as well.

"You go on inside," Steve repeated the words he had told Ellie earlier that evening, "I'll come in after a minute."

"All right, Dad," Chuck said quietly, grasping Steve's shoulder in a brief gesture of affinity, "all right." Then he turned to go inside with a last smile and nod.

Steve watched Chuck's retreating back, and a feeling welled up inside him so powerfully that he seemed to swell with it.

"Wait—Charles," he called out, unable to stop himself.

Chuck turned at the doorway, his hand on the knob.

Steve smiled slightly.

"I'm proud of you, son."

_End._

_AN—the major flaw in this story is that technically at this point in time, Chuck's still planning on running away with Sarah when he gets to Prague. From my view, though, I think Chuck was on the fence from the beginning. On one hand he has the girl he loves, and on the other he has something that he chose to do—something bigger than himself. He knows that if he joined Sarah, it would mean not only turning his back on all the good that he could do but also that he would forever be on the run, despite being with the person he loves. He could never see his family again—and that is what Chuck's all about. So for this conversation, Chuck's wavering toward not going with Sarah. _


End file.
